A method for selection and use of numerical integration points for molecules with cylindrical symmetry

Boys and Handy [1] have discussed the solution of the bivariational equations with restricted numerical integration. One of the weaknesses of the method was that in the numerical summations over points, some points arose with r _ij= 0 and non-zero weights. This makes the method quite impractical for the Schrodinger Hamiltonian (because of the singularity at r _ij= 0), and it cannot be advantageous for the transcorrelated Hamiltonian C^–1HC because there will be some discontinuous higher derivatives at r _ij=0. Here it is shown how the symmetry of cylindrically symmetric molecules can be used to eliminate such points, without losing any of the advantages of the overall method, such as the convergence of the eigensolutions. It is also shown how the primary numerical integration points (z _i, r_i) may be chosen in any calculation such that each is associated with an equal amount of one-electron density. The choice of the angular coordinates are governed by the removal of the r _ij=0 points and maintaining the natural orthogonality between orbitals of different symmetry types. The method has been programmed and found to be practical, although no new molecular calculations have yet been performed. It is to be hoped that these points will give a basis for new transcorrelated calculations on diatomic molecules.This paper was presented during the session on numerical integration methods for molecules of the 1970 Quantum Theory Conference in Nottingham. It has been revised in the light of the interesting discussion which followed.     

Deposition of Oral Bacteria and Polystyrene Particles to Quartz and Dental Enamel in a Parallel Plate and Stagnation Point Flow Chamber

The aim of this paper is to determine to what extent (i) deposition of oral bacteria and polystyrene particles, (ii) onto quartz and dental enamel with and without a salivary conditioning film, (iii) in a parallel plate (PP) and stagnation point (SP) flow chamber and at common Peclet numbers are comparable. All three bacterial strains showed different adhesion behaviors, and even Streptococcus mitis BMS, possessing a similar cell surface hydrophobicity as polystyrene particles, did not mimic polystyrene particles in its adhesion behavior, possibly as a result of the more negative ζ potentials of the polystyrene particles. The stationary endpoint adhesion of all strains, including polystyrene particles, was lower in the presence of a salivary conditioning film, while also desorption probabilities under flow were higher in the presence of a conditioning film than in its absence. Deposition onto quartz and enamel surfaces was different, but without a consistent trend valid for all strains and polystyrene particles. It is concluded that differences in experimental results exist, and the process of bacterial deposition to enamel surfaces cannot be modeled by using polystyrene particles and quartz collector surfaces.     

Incorporating the effect of ionic strength in free energy calculations using explicit ions

The incorporation of explicit ions to mimic the effect of ionic strength or to neutralize the overall charge on a system in free energy calculations using molecular dynamics simulations is investigated. The difference in the free energy of hydration between two triosephosphate isomerase inhibitors calculated at five different ion concentrations is used as an example. We show that the free energy difference can be highly sensitive to the presence of explicit ions even in cases where the mutation itself does not involve a change in the overall charge. The effect is most significant if the molecule carries a net charge close to the site mutated. Furthermore, it is shown that the introduction of a small number of ions can lead to very severe sampling problems suggesting that in practical calculations convergence can best be achieved by incorporating either no counterions or by simulating at high ionic strength to ensure sufficient sampling of the ion distribution.     

predForm-Site: Formylation site prediction by incorporating multiple features and resolving data imbalance

Formylation is one of the newly discovered post-translational modifications in lysine residue which is responsible for different kinds of diseases. In this work, a novel predictor, named predForm-Site, has been developed to predict formylation sites with higher accuracy. We have integrated multiple sequence features for developing a more informative representation of formylation sites. Moreover, decision function of the underlying classifier have been optimized on skewed formylation dataset during prediction model training for prediction quality improvement. On the dataset used by LFPred and Formator predictor, predForm-Site achieved 99.5% sensitivity, 99.8% specificity and 99.8% overall accuracy with AUC of 0.999 in the jackknife test. In the independent test, it has also achieved more than 97% sensitivity and 99% specificity. Similarly, in benchmarking with recent method CKSAAP_FormSite, the proposed predictor significantly outperformed in all the measures, particularly sensitivity by around 20%, specificity by nearly 30% and overall accuracy by more than 22%. These experimental results show that the proposed predForm-Site can be used as a complementary tool for the fast exploration of formylation sites. For convenience of the scientific community, predForm-Site has been deployed as an online tool, accessible at http://103.99.176.239:8080/predForm-Site.     

多柱色谱技术进展

在色谱分析过程中，利用串联、并联或串并联结合的方式将多根色谱柱组合起来，可以实现高通量和高分辨的分离效果。相比于传统单柱色谱技术，多柱技术很好地满足了批量样品分析和复杂生物样品分离分析的需求，因此引起了广泛关注。该文对多柱技术在多维分离、芯片色谱、毛细管电泳、固定相筛选以及串联色谱等领域的应用进行了综述，并对其发展前景进行了展望。     

集成滤波器在谱图信号除噪中的应用

本文提出了一种由神经元网络与线性自适应滤波器组成的集成滤波器的实现方法，用于谱图信号除噪处理。     

基于知识体系整合的元素无机化学教学改革

元素无机化学是大学化学及相关专业无机化学课程的核心内容。如何教好、学好元素无机化学的知识一直是教学工作者研究的课题。为改变教学现状，提高教学效果，培养学生的逻辑思维和科学创新能力，提出一种整合元素无机化学知识的思路，即：以化合物类型为主线对元素无机化学知识进行系统化整合，并以氧化物部分为例加以说明。     

基于国际化产科教融合实训平台的教学模式改革与实践

在分析当前省属工科院校教育以能力为导向培养目标完成实施过程中遇到国际化困难问题的基础上，以青岛大学材料学科为例，提出了基于国际化产科教融合实训平台的教学模式改革举措，并经过实践验证证实其切实可行。包括：充分整合校内外材料学科整体资源，建立了国际化的产科教深度融合实训平台，构建了高效的国际化产科教深度融合协同育人实训平台动态管理运行机制；以实训平台为依托实现师资队伍、教学内容、教学模式、科研等全方位的国际化改革；基于国际化产教研融合实训平台的教学模式改革的实践收到显著成效，对全国省属高等院校理工学科专业建设国际化改革的推广有较好的示范作用。     

Simple algorithm for isothermal-isobaric molecular dynamics

We review principles of non-Hamiltonian statistical mechanics and present a new set of equations and integration algorithm for isothermal-isobaric dynamics. The chief advantage of the present scheme is that it is somewhat simpler than previous methods. We perform numerical simulations to test the accuracy of the algorithm and compare its stability to that of a "gold standard," a symplectic integrator for Hamiltonian dynamics of the same system. The stability of the isothermal-isobaric algorithm is comparable to the stability of the symplectic integrator.     

Fast folding and comparison of RNA secondary structures

Summary Computer codes for computation and comparison of RNA secondary structures, the Vienna RNA package, are presented, that are based on dynamic programming algorithms and aim at predictions of structures with minimum free energies as well as at computations of the equilibrium partition functions and base pairing probabilities.An efficient heuristic for the inverse folding problem of RNA is introduced. In addition we present compact and efficient programs for the comparison of RNA secondary structures based on tree editing and alignment.All computer codes are written in ANSI C. They include implementations of modified algorithms on parallel computers with distributed memory. Performance analysis carried out on an Intel Hypercube shows that parallel computing becomes gradually more and more efficient the longer the sequences are.

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Schnelle Faltung und Vergleich von Sekundärstrukturen von RNA

Zusammenfassung Die im Vienna RNA package enthaltenen Computer Programme für die Berechnung und den Vergleich von RNA Sekundärstrukturen werden präsentiert. Ihren Kern bilden Algorithmen zur Vorhersage von Strukturen minimaler Energie sowie zur Berechnung von Zustandssumme und Basenpaarungswahrscheinlichkeiten mittels dynamischer Programmierung.Ein effizienter heuristischer Algorithmus für das inverse Faltungsproblem wird vorgestellt. Darüberhinaus präsentieren wir kompakte und effiziente Programme zum Vergleich von RNA Sekundärstrukturen durch Baum-Editierung und Alignierung.Alle Programme sind in ANSI C geschrieben, darunter auch eine Implementation des Faltungs-algorithmus für Parallelrechner mit verteiltem Speicher. Wie Tests auf einem Intel Hypercube zeigen, wird das Parallelrechnen umso effizienter je länger die Sequenzen sind.